SMTL ID : 8sar.1

CryoEM structure of DH270.6-CH848.10.17

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 13 residues within 4Å: Chain A: N.263, N.264, T.265, I.284 Chain C: R.62, Y.110 Chain D: S.2, T.25, Y.27, H.32, F.93, G.95, S.96 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.5: 12 residues within 4Å: Chain E: N.263, N.264, T.265, I.284 Chain G: Y.110 Chain H: S.2, T.25, Y.27, H.32, F.93, G.95, S.96 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.9: 12 residues within 4Å: Chain I: N.263, N.264, T.265, I.284 Chain K: Y.110 Chain L: S.2, T.25, Y.27, H.32, F.93, G.95, S.96 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.2: 21 residues within 4Å: Chain A: T.259, H.291, N.293, T.371, T.373 Chain C: G.26, Y.27, T.28, D.31, W.101, S.103, Y.105, Y.106, Y.111, N.113, D.115 Chain D: Y.48, Y.51, R.56, P.57, S.58 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.26, C:T.28, C:D.31 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.10: 20 residues within 4Å: Chain I: T.259, H.291, N.293, T.371, T.373 Chain K: G.26, Y.27, T.28, D.31, W.101, S.103, Y.105, Y.106, Y.111, N.113 Chain L: Y.48, Y.51, R.56, P.57, S.58 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:G.26, K:T.28, K:D.31

5 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 5 residues within 4Å: Chain A: T.105, V.106, N.116, Y.133, L.135 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain E: T.105, V.106, N.116, Y.133, L.135 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain E: N.400, T.402 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 6 residues within 4Å: Chain I: T.105, V.106, N.116, Y.133, L.135, D.282 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain I: N.400, T.402 Chain L: H.32, D.33, L.34 1 PLIP interactions: 1 interactions with chain L Hydrophobic interactions: L:L.34

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.4: 2 residues within 4Å: Chain A: N.400, T.402 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.6: 20 residues within 4Å: Chain E: T.259, H.291, N.293, T.371, T.373 Chain G: G.26, Y.27, T.28, D.31, W.101, S.103, Y.105, Y.106, Y.111, N.113 Chain H: Y.48, Y.51, R.56, P.57, S.58 No protein-ligand interaction detected (PLIP)

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.13: 4 residues within 4Å: Chain A: N.108 Chain C: T.69, M.70, T.71 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:M.70, C:M.70 NAG.14: 5 residues within 4Å: Chain E: N.108 Chain G: T.69, M.70, T.71, E.82 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain G Hydrogen bonds: E:N.108, G:M.70, G:M.70 NAG.15: 5 residues within 4Å: Chain I: N.108 Chain K: T.69, M.70, T.71, E.82 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:M.70, K:E.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Henderson, R. et al., Structural basis for breadth development in the HIV-1 V3-glycan targeting DH270 antibody clonal lineage. Nat Commun (2023)

Release Date

2023-04-19

Peptides

CH848.10.17 gp120: AEI
CH848.10.17 gp41: BFJ
DH270.6 variable heavy chain: CGK
DH270.6 variable light chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
F

I
K

B
B

F
G

J
L

C
C

G
H

K
M

D
D

H
I

L
N

CH848.10.17 gp120

CH848.10.17 gp41

DH270.6 variable heavy chain

DH270.6 variable light chain

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